1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
|
Kinetics Modeling in GENESIS
The kinetics C-code library and kinetikit.
Version 1.2
By Upinder S. Bhalla
Copyright 1994-1997
National Centre for Biological Sciences, Bangalore, INDIA
Kinetikit is a utility for modeling large numbers of chemical reactions
such as occur in biochemical signaling pathways. It consists of two
sections: the C-code library kinetics, which gets compiled and linked with
GENESIS, and the script interface for Kinetikit, also known as kkit.
These files are copylefted, that is, copyrighted under the GNU Public
License (the kinetics library is copyrighted under the GNU Library
Public License, which is very similar, only it applies to libraries rather
than stand-alone programs). Please see the file COPYRIGHT for details.
kkit1.1 requires GENESIS version 2.0.1 or greater, plus the kinetics library.
As of GENESIS version 2.1, the kinetics library is compiled into GENESIS by
default. The installation procedure for older versions of GENESIS is
described in the kinetikit distribution, available from the usual GENESIS
distribution sites.
=============================================================================
In addition to the scripts used for running Kinetikit this directory contains
the following files or directories:
README - You're reading it!
tutorial.doc - A tutorial document in Microsoft Word 6.0
COPYRIGHT - The copyright notice.
Kkit.help - The directions for kkit, viewable from within kkit.
kkit.g - The main script for running kkit.
Kinetikit.g - An alias for kkit.g
examples/ - Directory of example scripts for use with kkit.
examples/README - Description of the example scripts.
=============================================================================
Using Kinetikit:
If you plan to use kinetikit frequently as a tool, add the kinetikit
directory to your SIMPATH in the .simrc file,just as you would for other
'kits' like Neurokit. A typical path would now look like:
setenv SIMPATH . \
/home/myname/genesis/Scripts/kinetikit
To try out Kinetikit, go to the kinetikit directory (this one), and type
'genesis kkit'. If the installation has been successful, then an information
note containing copyright information and the Statement on Models and
Experiments should appear while Kinetikit loads. Then the Kinetikit interface
should pop up, and you are set to start modeling. Refer to the help file in
this directory (which is also accessible from within Kinetikit) for further
information on using it.
For further information about the use of Kinetikit and modeling of biochemical
kinetics, see Chapter 10, of "The Book of GENESIS", second edition. The
documentation for the GENESIS objects pool, enz, reac, and concchan will be
helpful for using these kinetics objects in GENESIS simulations outside of
Kinetikit.
=============================================================================
Notes for users of kkit 1.0
---------------------------
Changes from version 1.0
1. Added facility to allow batch-mode (no graphics) running for models.
2. Greatly improved documentation in the help file.
3. Improved implementation of the xtab, including file loading and more
waveform manipulation options.
4. The kinetics library is now set up to compile as a user library, rather
than as part of the main Genesis code tree.
Users of the earlier 1.0 release of kkit will not have to make any GENESIS
code changes to get it to run if they are in a hurry, but there are
recommended changes for some of the newer features to work properly.
Also, a number of bugs in the old code have been fixed.
Models saved using the old kkit will load normally into this version, and
most files written with this version will load into the old one.
=============================================================================
Notes for users of kkit 1.1
---------------------------
Changes from version 1.1
1. New tool added for comparing models
2. The 'Cooperative reactions' label has been corrected to 'Higher order'
reactions.
3. Options added to directly modulate kf and kb for reactions.
4. Sundry updates to the 'Help' file, and minor bugfixes.
5. Tutorial document. This will also appear in revised form in the Book
of Genesis, 2nd edition.
Models saved using the kkit1.1 will load normally into this version, and
most files written with this version will load into kkit1.1 in the unlikely
event that you want to go backwards.
The C code has not changed since the earlier release, so recompilation
should not be necessary.
=============================================================================
Note on future development:
At present kkit is designed as a stand-alone program. Future development will
involve conversion to the standard 'kit' format which is used for SoN (Son of
Neurokit, or Neurokit 2) and for other 'kits'. Ambitious users who mess with
the scripts should therefore be aware that there will be major changes in the
script code, although not in the interface itself.
=============================================================================
Bug reports:
------------
Please send bug reports relating to kinetikit (and only to kinetikit) to
bhalla@ncbs.tifrbng.res.in
I cannot guarantee a quick reply, but I will try to fix things as they
turn up. Please do _not_ send me general questions regarding GENESIS and
its installation. These are more appropriately addressed to the GENESIS
address: genesis@bbb.caltech.edu
=============================================================================
|
